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Microbial Community Analysis in Soil (Rhizosphere) and the Marine (Plastisphere) Environment in Function of Plant Health and Biofilm Formation

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Microbial Community Analysis in Soil (Rhizosphere) and the Marine (Plastisphere) Environment in Function of Plant Health and Biofilm Formation Microbial community analysis in soil (rhizosphere) and the marine (plastisphere) environment in function of plant health and biofilm formation Caroline De Tender Thesis submitted in fulfillment of the requirements for the degree of Doctor (PhD) in Biotechnology Promotors: Prof. Dr. Peter Dawyndt Department of Applied mathematics, Computer Science and Statistics Faculty of Science Ghent University Dr. Martine Maes Crop Protection - Plant Sciences Unit Institute for Agricultural, Fisheries and Food Research (ILVO) Ir. Lisa Devriese Fisheries – Animal Sciences Unit Insitute for Agricultural, Fisheries and Food Research (ILVO) Dank je wel! De allerlaatste woorden die geschreven worden voor deze thesis zijn waarschijnlijk de eerste die gelezen worden door velen. Ongeveer vier jaar geleden startte ik mijn doctoraat bij het ILVO. Met volle moed begon ik aan mijn avontuur. Het ging niet altijd even vlot en ik kan eerlijk bekennen dat meerdere grenzen verlegd zijn. Vooral de combinatie van twee onderwerpen bleek niet altijd evident en kostte me meer dan eens bloed, zweet en tranen. Daarentegen bracht het ook vele opportuniteiten. De enige dag kon ik aan het wroeten zijn in de serre, terwijl ik de dag erop op de Simon Stevin sprong (en dit mag letterlijk worden genomen!) om plastic uit zee te vissen. Ja, het was me wel het avontuur… Natuurlijk zou dit allemaal niet mogelijk geweest zijn zonder de hulp van een aantal geweldige mensen. In de eerste plaats, mijn promotoren: Prof. Peter Dawyndt, dr. Martine Maes en natuurlijk Lisa Devriese. Dank je wel om vier jaar geleden het vertrouwen te hebben om mij dit onderzoek toe te wijzen, me steeds in de juiste richting te duwen als ik het Noorden even kwijt was, maar ook voor de gezellige babbels op de bureau. Daarnaast had ik ook een geweldige begeleidster voor mijn rhizosfeer luik. Jane, ik zal nooit het moment vergeten in januari 2017 toen ik in halve paniek je bureau binnenliep over een hoofdstuk rond biochar. Jij bleef rustig en je woorden: “No panic, biochar is my middle name” zullen steeds in mijn geheugen gegrift staan. Bedankt om er al die jaren voor mij te zijn! Ik kan eerlijk zeggen dat ik me dankzij jou meteen thuis voelde op het ILVO. Daarbij wil ik ook Lisa nog eens bedanken, want naast promotor ben je ook de eerste twee jaar mijn begeleidster geweest. Van wilde plannen voor ons blootstellingsexperiment (herinner: we gooien een hondenbench met plastic in het water) tot onze broodjes lunch over de middag, het was een mooie tijd! Ook had ik twee fantastische laboranten (mijn persoonlijke superman en superwoman) en een supertechnieker aan mijn zijde. Als ik in Oostende aan het knoeien was met touwen te knopen, stond Pieter mijn aardbeiplantjes water te geven. In het prille begin heeft hij me wegwijs moeten maken in het labo in Merelbeke en ondanks dat ik de eerste keer mijn DNA extractie in de mist liet lopen (wie had er gedacht dat je buisje 2 en 3 niet mocht wisselen met elkaar), bleef hij altijd rustig. Pieter, ons geknoei met de potgrond en de rhizosfeer zullen niet snel uit mijn geheugen gebannen worden! Bedankt om er steeds te zijn. Op deze momenten dat het tijd was om de rhizosfeer stalen te verzamelen in Merelbeke, kon ik rekenen op Sara om mijn plastic stalen te verzamelen en in weer in wind op zee te trekken. Sara, je bent een superlaborante en ik hoop ooit net zo zelfverzekerd in het labo te staan. Lang leve onze gezellige momenten in de keuken van de Simon Stevin en het heen en weer geklots op de zodiac. III Het blootstellingsexperiment op zee had er niet geweest zonder 1 specifieke persoon: Kevin. Je hebt er wel heel wat blaren, kneuzen en gezaag van mij voor moeten doorstaan (“is het nu nog niet klaar Kevin…”), dankzij jouw handige vingers zijn die constructies toch in zee geraakt! Ook nog een speciaal bedankje aan de mensen van het Genomics team die me steeds ondersteunden en meer specifiek onze twee specialisten: Annelies en Tom. Jullie mailbox werd soms bestookt met honderden vragen, maar dankzij jullie hulp ben ik niet alleen beter geworden in programmeren, maar ook in me te verdedigen (probeer het maar eens te winnen van een (soms relatief koppige) hollander…). Daarnaast wil ik uiteraard al mijn ILVO collega’s bedanken voor de gezellige tijd, de toffe babbels tijdens het eten, de vele leuke uitstapjes (frituur, een amadeuske, etc.). Vooral de cx- namiddagen met de sportieve mensen van P96 zullen me lang bijblijven. Met uitzondering van 1 persoon ga ik verder niemand bij naam noemen (want ik zou het niet over mijn hart krijgen dat ik iemand vergeet), maar mijn bureau-, cx- en gezellig-moment-babbel genootje Inge kan ik toch niet overschieten. In de laatste maanden ben je zeker een rots in de branding geweest op het ILVO. Je hebt me geleerd om rustig te blijven, mijn oneindige verhalen van de trouw en de bouw doorstaan en me soms vanachter mijn computer gehaald om te gaan wokken! Gewoon een super collega en vriendin. Mijn vrienden en familie kan ik uiteraard ook niet vergeten. Ze boden niet alleen mentale steun tijdens de periode, maar zelfs praktische (wat azobé hout van nonkel Rudi en tante Carin, hulp van mijn broer voor de constructies uit te tekenen, Clara met haar geweldige tekentalent). Vooral mijn ouders en mijn fantastische broer Steven wil ik bedanken. Zij zijn er al die jaren voor mij geweest en hebben me steeds gesteund in alles wat ik doe. Steven, er werd soms wat over- en weer geplaagd, maar uit de grond van mijn hart, je bent en blijft de beste broer ter wereld! Mama en papa, nog eens extra bedankt voor jullie. Papa mijn doorzettingsvermogen heb ik helemaal aan jou te danken. Mama, bedankt dat je geregeld bijsprong in het huishouden de laatste maanden. En dan als laatste, Jeroen, ondertussen mijn man (wat doet dat raar om te zeggen). Schat, het was een helse maand voor ons. Een huis bouwen, een trouw op poten zetten en dan kwam die doctoraatsverdediging er nog bij. Meer dan eens kwam je toe in een niet opgeruimd huis, moest je zelf je potje nog opwarmen na een harde dag werk op de bouw, maar niet één keer heb je geklaagd. Ik beloof je dat ik er vanaf nu meer zal zijn en kijk er enorm naar uit om aan ons getrouwd leven samen te beginnen. Want dankzij jouw steun en stevige schouder om af en toe eens op te huilen (het waren écht zware maanden) ga ik nu niet alleen door het leven als “mevrouw De Visscher”, maar kan ik me binnenkort ook met enige trots “Doctor” noemen. IV CONTENTS LIST OF ACRONYMS AND ABBREVIATIONS .................................................................................. VII Summary .................................................................................................................................... IX Samenvatting ............................................................................................................................ XIII Preface ..................................................................................................................................... XIX Chapter 1 General introduction .................................................................................................... 1 1.1 ENVIRONMENTAL MICROBIOLOGY ............................................................................................... 3 1.2 ENVIRONMENT 1: THE RHIZOSPHERE ......................................................................................... 11 1.3 ENVIRONMENT 2: THE PLASTISPHERE ........................................................................................ 20 Problem statement and thesis outline ........................................................................................ 27 Part I THE RHIZOSPHERE ............................................................................................................... 33 Chapter 2 Rhizosphere microbiome in response to biochar .......................................................... 35 2.1 MATERIALS AND METHODS......................................................................................................... 39 2.2 RESULTS ....................................................................................................................................... 50 2.3 DISCUSSION AND CONCLUSIONS ................................................................................................ 58 Chapter 3 Dynamics of the rhizosphere microbiome in response to biochar ................................. 67 3.1 MATERIALS AND METHODS......................................................................................................... 71 3.2 RESULTS ....................................................................................................................................... 77 3.3 DISCUSSION AND CONCLUSIONS ................................................................................................ 89 Chapter 4 Rhizosphere microbiome in response to chitin ............................................................. 95 4.1 MATERIALS AND METHODS......................................................................................................... 99 4.2 RESULTS ..................................................................................................................................... 107 4.3 DISCUSSION AND CONCLUSIONS .............................................................................................. 118 Part II THE PLASTISPHERE .......................................................................................................... 127 Chapter 5 Bacterial community profiling of marine plastic
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